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    Document   : redbluepka
    Created on : Dec 4, 2008, 5:33:43 PM
    Author     : Annamaria Jakab
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    <title>Red and blue annotation of pKa</title>
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  <h1>Red and blue annotation of p<i>K</i><sub>a</sub></h1>
  
  <p>  
  The <b>static (default setting) <font color="red">red</font> &amp; <font color="blue">blue</font> colour annotation</b> is related to the following ionization steps:
  <table align="center">
    <tr><td><img src="pKa_files/redblue1.png" width="333" height="145"></td></tr>
</table>
  
  The <b>static <font color="red">red</font> &amp; <font color="blue">blue</font> coloring schema</b> does not depend on which ionic form 
of a molecule is submitted to the pKa calculation.
 The next three species have the same pKa value and the same color.

  <table align="center">
    <caption><small><b>Calculated pKa of the deprotonated, neutral, and the protonated
 forms of ammonia 
according to the static <font color="red">red</font> &amp; <font color="blue">blue</font>
coloring schema</b></small></caption>
<tr><td><img src="pKa_files/redblue2.png" width="253" height="111">
</td></tr>
  </table>

<p> 

The <b>dynamic (non-default setting) <font color="red">red</font> &amp; <font color="blue">blue</font>
coloring schema</b> depends on the <font color=#CC9900><b>submitted molecule</b></font>:
   <table align="center">
   <tr><td>
  <img src="pKa_files/redblue4.png" width="509" height="267"></td></tr>
</table>
<p>
 

<p>The result of the previous ammonia example with the non-default p<i>K</i><sub>a</sub> 
calculation:

  <table align="center">
    <caption><small><b>Calculated pKa of deprotonated, neutral, and the protonated forms of ammonia
according to the dynamic <font color="red">red</font> &amp; <font color="blue">blue</font>
coloring schema</b></small></caption>
    <tr><td><img src="pKa_files/redblue6.png" width="256" height="114"></td></tr>
</table>
  
  <p>Differences between the <b>static</b> and the <b>dynamic 
  <font color="red">red</font> &amp; <font color="blue">blue</font></b> coloring schema:</p>
  
  <table width=65% border="1">
<thead>
<tr>
<th width=20%></th>
<th width=30%>static</th>
<th width=30%>dynamic</th>
</tr>
</thead>
<tbody>
<tr>
<td>Subject of calculation</td>
<td>neutral state of the submitted molecule</td>
<td>the submitted molecule</td>
</tr>
<tr>
<td><font color="blue">Blue color</font> assigned to</td>
<td>the acid dissociation constant between the  
neutral base and its conjugated acid</td>
<td>the acid dissociation constant between the  
submitted base and its conjugated acid</td>
</tr>
<tr>
<td><font color="red">Red color</font> assigned to</td>
<td> the acid dissociation constant between the  
neutral acid and its conjugated base</td>
<td> the acid dissociation constant between the  
submitted acid and its conjugated base</td>
</tr>
<tr>
<td>setting in the Options panel</td>
<td align="center"><img src="pKa_files/redblue7.png" width="199" height="380" alt="redblue9"/>
</td>
<td align="center"><img src="pKa_files/redblue8.png" width="199" height="380" alt="redblue10"/>
</td>
</tr>
</tbody>
</table>

  
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